Research workbench
Cryo-EM structure of tetrameric PTCH1 in complex with shhnp (form I)
Analyse Cryo-EM structure of tetrameric PTCH1 in complex with shhnp (form I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N7G
- Type
- protein
- Length
- 4,306 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1; Sonic hedgehog protein
- UniProt
- Q13635, Q15465
- Ligands
- CLR, PLM, NAG, CA, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein patched homolog 1 | protein | 991 | 53% helix, 6% strand | Q13635 |
| B, E | Protein patched homolog 1 | protein | 988 | 52% helix, 5% strand | Q13635 |
| C, F | Sonic hedgehog protein | protein | 174 | 20% helix, 15% strand | Q15465 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 10 copies · chains A, B, C, D, E, F
- PLM · Palmitic acid · ligand · 2 copies · chains B, C, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B, D, E
- CA · Calcium ion · metal · 4 copies · chains C, F
- ZN · Zinc ion · metal · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.88 | 0.91 | 79 | CLR |
| 2 | 699 | 0.88 | 0.91 | 72 | CLR |
| 3 | 540 | 0.86 | 0.92 | 61 | CLR |
| 4 | 366 | 0.86 | 0.94 | 49 | PLM |
| 5 | 532 | 0.86 | 0.92 | 61 | CLR |
Interfaces
5 interfaces between chains.
- E–F · 2320 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2313 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1218 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1214 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 56 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 12 disulfide, 4 covalent, 4 lipid (N-glycosylation, disulfide, covalent ligand, palmitoylation).
Compared structures
- 6N7G · Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form I) · the same entry in another collection · chain F against F, TM-score 1.00
- Q13635 · AlphaFold monomer V2.0 prediction for protein patched homolog 1 (Q13635) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q15465 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q15465) · a predicted model of the same protein · chain C against A, TM-score 0.88
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q13635
- Every structure of UniProt Q15465
- Elsewhere: RCSB PDB 6N7G · PDBe 6N7G · UniProt Q13635 · UniProt Q15465
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.